A. CDKN2 alterations commonly occur in lung cancer. To identify pharmacologic agents that might mimic the cdk4:cyclin D kinase inhibitory activity of the DCKN2 gene product (p16INK4A), the 60 cell lines of the NCI drug screen program were studied for biallelic deletions, intragenic mutations, and transcriptional suppression of CDKN2. Agents from among the more than 50,000 compounds screened for activity that induce greater growth suppression in the 47 CDKN2-altered cell lines than in the 13 CDKN2 normal cell lines were identified using the COMPARE algorithm. The agent with the best correlation with p16 status was found to inhibit cdk4:cyclin D1 in vitro. B. The methylthioadenosine phosphorylase (MTAP) gene is located about 100 kb telemetric to CDKN2 on chromosome 9 and was determined to be codeleted with CDKN2 in about two-thirds of 60 cell lines with deletion of CDKN2 and in none of 44 cell lines without CDKN2 deletion. Functional MTAP activity was detected only in cell lines with retained MTAP gene. Using a 4 day MTT assay, the mean of the IC50's of several inhibitors of de novo purine synthesis was determined to be about 10-fold lower among 6 MTAP-negative cell lines compared with 6 MTAP-positive cell lines. The toxicity of de novo purine synthesis inhibitors was decreased by the addition of MTA, the substrate for MTAP-positive but not MTAP-negative cells. C. An aberrant-sized LMYC-containing cDNA in the LMYC amplified SCLC cell line, NCI-H378, was found to contain sequences of a novel cyclophilin-like gene that is coamplified with LMYC in 7 of 11 LMYC amplified cell lines compared with amplification of the RFL gene in 4 of these 11 lines.